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Various improvement in documentation and a decoding function (#6383)

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* Various improvement in documentation and a decoding function

- Improves documentation on the type size when creating/accessing a compound datatype with no predefined struct (GH issue #5371)
- Provides better description of the min_meta_perc and min_raw_perc arguments in the H5Pset_page_buffer_size() (GH issue #5711)
- Adds error checkings to an internal decoding function

* Corrected the checks, the base address equals the end-of-file is valid.

* Skip for multi-file and split drivers when validating addresses against stored_eof

* Committing clang-format changes

* Remove incorrect name

* Fix typos

* Modified description of type_size arguments

* Used a more robust condition when checking EOF

* Corrected incorrect conflict resolving

* Update src/H5Fsuper_cache.c

Co-authored-by: Neil Fortner <fortnern@gmail.com>

* Update src/H5Fsuper_cache.c

Co-authored-by: Neil Fortner <fortnern@gmail.com>

* Committing clang-format changes

* Modified per feedbacks.

* Fix comparison per feedbacks

* Omit unused parameter name in a catch block

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Neil Fortner <fortnern@gmail.com>
This commit is contained in:
bmribler
2026-07-21 16:54:08 -04:00
committed by GitHub
co-authored by Neil Fortner github-actions
parent 400de1dc95
commit 1da455e53a
7 changed files with 118 additions and 20 deletions
Download Patch File Download Diff File Expand all files Collapse all files
c++/src/H5StrType.cpp
+1 -1
View File
@@ -194,7 +194,7 @@ StrType::decode() const
try {
encoded_strtype_id = p_decode();
}
catch (DataTypeIException &err) {
catch (DataTypeIException &) {
throw;
}
StrType *encoded_strtype = new StrType;
c++/src/H5VarLenType.cpp
+1 -1
View File
@@ -138,7 +138,7 @@ VarLenType::decode() const
try {
encoded_vltype_id = p_decode();
}
catch (DataTypeIException &err) {
catch (DataTypeIException &) {
throw;
}
VarLenType *encoded_vltype = new VarLenType;
hl/src/H5TBpublic.h
+49 -16
View File
@@ -139,8 +139,7 @@ extern "C" {
* \param[in] nfields The number of fields
* \param[in] nrecords The number of records
* \param[in] type_size The size in bytes of the structure
* associated with the table;
* This value is obtained with \c sizeof().
* associated with the table
* \param[in] field_names An array containing the names of the fields.
* Names longer than #HLTB_MAX_FIELD_LEN - 1 characters
* are silently truncated when read back by
@@ -160,6 +159,12 @@ extern "C" {
* \p dset_name attached to the object specified by the
* identifier loc_id.
*
* \p type_size can be obtained with \c sizeof(), if the data is
* stored in a predefined C struct. Otherwise, \p type_size should
* be calculated based on the highest offset in \p field_offset, the
* size of its corresponding datatype in \p field_types, and any
* padding bytes desired after that field.
*
*/
H5HL_DLL herr_t H5TBmake_table(const char *table_title, hid_t loc_id, const char *dset_name, hsize_t nfields,
hsize_t nrecords, size_t type_size, const char *field_names[],
@@ -182,8 +187,7 @@ H5HL_DLL herr_t H5TBmake_table(const char *table_title, hid_t loc_id, const char
* \fg_loc_id
* \param[in] dset_name The name of the dataset to overwrite
* \param[in] nrecords The number of records to append
* \param[in] type_size The size of the structure type,
* as calculated by \c sizeof().
* \param[in] type_size The size of the structure type
* \param[in] field_offset An array containing the offsets of
* the fields. These offsets can be
* calculated with the #HOFFSET macro
@@ -198,6 +202,10 @@ H5HL_DLL herr_t H5TBmake_table(const char *table_title, hid_t loc_id, const char
* identifier \p loc_id. The dataset is extended to hold the
* new records.
*
* \p type_size can be obtained with \c sizeof(), if the data is
* stored in a predefined C struct. Otherwise, it can be obtained
* by calling H5TBget_field_info() if not already known.
*
*/
H5HL_DLL herr_t H5TBappend_records(hid_t loc_id, const char *dset_name, hsize_t nrecords, size_t type_size,
const size_t *field_offset, const size_t *dst_sizes, const void *buf);
@@ -212,8 +220,7 @@ H5HL_DLL herr_t H5TBappend_records(hid_t loc_id, const char *dset_name, hsize_t
* \param[in] dset_name The name of the dataset to overwrite
* \param[in] start The zero index record to start writing
* \param[in] nrecords The number of records to write
* \param[in] type_size The size of the structure type, as
* calculated by \c sizeof().
* \param[in] type_size The size of the structure type
* \param[in] field_offset An array containing the offsets of
* the fields. These offsets can be
* calculated with the #HOFFSET macro
@@ -227,6 +234,10 @@ H5HL_DLL herr_t H5TBappend_records(hid_t loc_id, const char *dset_name, hsize_t
* index position start of the table named \p dset_name attached
* to the object specified by the identifier \p loc_id.
*
* \p type_size can be obtained with \c sizeof(), if the data is
* stored in a predefined C struct. Otherwise, it can be obtained
* by calling H5TBget_field_info() if not already known.
*
*/
H5HL_DLL herr_t H5TBwrite_records(hid_t loc_id, const char *dset_name, hsize_t start, hsize_t nrecords,
size_t type_size, const size_t *field_offset, const size_t *dst_sizes,
@@ -243,8 +254,7 @@ H5HL_DLL herr_t H5TBwrite_records(hid_t loc_id, const char *dset_name, hsize_t s
* \param[in] field_names The names of the fields to write
* \param[in] start The zero index record to start writing
* \param[in] nrecords The number of records to write
* \param[in] type_size The size of the structure type, as
* calculated by \c sizeof().
* \param[in] type_size The size of the structure type
* \param[in] field_offset An array containing the offsets of
* the fields. These offsets can be
* calculated with the #HOFFSET macro
@@ -259,6 +269,10 @@ H5HL_DLL herr_t H5TBwrite_records(hid_t loc_id, const char *dset_name, hsize_t s
* dataset named \p dset_name attached to the object specified
* by the identifier \p loc_id.
*
* \p type_size can be obtained with \c sizeof(), if the data is
* stored in a predefined C struct. Otherwise, it can be obtained
* by calling H5TBget_field_info() if not already known.
*
*/
H5HL_DLL herr_t H5TBwrite_fields_name(hid_t loc_id, const char *dset_name, const char *field_names,
hsize_t start, hsize_t nrecords, size_t type_size,
@@ -278,8 +292,7 @@ H5HL_DLL herr_t H5TBwrite_fields_name(hid_t loc_id, const char *dset_name, const
* \param[in] field_index The indexes of the fields to write
* \param[in] start The zero based index record to start writing
* \param[in] nrecords The number of records to write
* \param[in] type_size The size of the structure type, as
* calculated by \c sizeof().
* \param[in] type_size The size of the structure type
* \param[in] field_offset An array containing the offsets of
* the fields. These offsets can be
* calculated with the #HOFFSET macro
@@ -294,6 +307,10 @@ H5HL_DLL herr_t H5TBwrite_fields_name(hid_t loc_id, const char *dset_name, const
* dataset named \p dset_name attached to the object
* specified by the identifier \p loc_id.
*
* \p type_size can be obtained with \c sizeof(), if the data is
* stored in a predefined C struct. Otherwise, it can be obtained
* by calling H5TBget_field_info() if not already known.
*
*/
H5HL_DLL herr_t H5TBwrite_fields_index(hid_t loc_id, const char *dset_name, hsize_t nfields,
const int *field_index, hsize_t start, hsize_t nrecords,
@@ -315,8 +332,7 @@ H5HL_DLL herr_t H5TBwrite_fields_index(hid_t loc_id, const char *dset_name, hsiz
*
* \fg_loc_id
* \param[in] dset_name The name of the dataset to read
* \param[in] dst_size The size of the structure type,
* as calculated by \c sizeof()
* \param[in] dst_size The size of the structure type
* \param[in] dst_offset An array containing the offsets of
* the fields. These offsets can be
* calculated with the #HOFFSET macro
@@ -331,6 +347,10 @@ H5HL_DLL herr_t H5TBwrite_fields_index(hid_t loc_id, const char *dset_name, hsiz
* \p dset_name attached to the object specified by
* the identifier \p loc_id.
*
* \p dst_size can be obtained with \c sizeof(), if the data is
* stored in a predefined C struct. Otherwise, it can be obtained
* by calling H5TBget_field_info() if not already known.
*
*/
H5HL_DLL herr_t H5TBread_table(hid_t loc_id, const char *dset_name, size_t dst_size, const size_t *dst_offset,
const size_t *dst_sizes, void *dst_buf);
@@ -349,7 +369,6 @@ H5HL_DLL herr_t H5TBread_table(hid_t loc_id, const char *dset_name, size_t dst_s
* \param[in] nrecords The number of records to read
* \param[in] type_size The size in bytes of the structure associated
* with the table
* (This value is obtained with \c sizeof().)
* \param[in] field_offset An array containing the offsets of the fields
* \param[in] dst_sizes An array containing the size in bytes of
* the fields
@@ -361,6 +380,10 @@ H5HL_DLL herr_t H5TBread_table(hid_t loc_id, const char *dset_name, size_t dst_s
* by \p field_names from a dataset named \p dset_name
* attached to the object specified by the identifier \p loc_id.
*
* \p type_size can be obtained with \c sizeof(), if the data is
* stored in a predefined C struct. Otherwise, it can be obtained
* by calling H5TBget_field_info() if not already known.
*
*/
H5HL_DLL herr_t H5TBread_fields_name(hid_t loc_id, const char *dset_name, const char *field_names,
hsize_t start, hsize_t nrecords, size_t type_size,
@@ -384,7 +407,6 @@ H5HL_DLL herr_t H5TBread_fields_name(hid_t loc_id, const char *dset_name, const
* \param[in] nrecords The number of records to read
* \param[in] type_size The size in bytes of the structure associated
* with the table
* (This value is obtained with \c sizeof())
* \param[in] field_offset An array containing the offsets of the fields
* \param[in] dst_sizes An array containing the size in bytes of
* the fields
@@ -396,6 +418,10 @@ H5HL_DLL herr_t H5TBread_fields_name(hid_t loc_id, const char *dset_name, const
* by \p field_index from a dataset named \p dset_name attached
* to the object specified by the identifier \p loc_id.
*
* \p type_size can be obtained with \c sizeof(), if the data is
* stored in a predefined C struct. Otherwise, it can be obtained
* by calling H5TBget_field_info() if not already known.
*
*/
H5HL_DLL herr_t H5TBread_fields_index(hid_t loc_id, const char *dset_name, hsize_t nfields,
const int *field_index, hsize_t start, hsize_t nrecords,
@@ -413,8 +439,7 @@ H5HL_DLL herr_t H5TBread_fields_index(hid_t loc_id, const char *dset_name, hsize
* \param[in] dset_name The name of the dataset to read
* \param[in] start The start record to read from
* \param[in] nrecords The number of records to read
* \param[in] type_size The size of the structure type,
* as calculated by \c sizeof()
* \param[in] type_size The size of the structure type
* \param[in] dst_offset An array containing the offsets of the
* fields. These offsets can be calculated
* with the #HOFFSET macro
@@ -428,6 +453,10 @@ H5HL_DLL herr_t H5TBread_fields_index(hid_t loc_id, const char *dset_name, hsize
* named \p dset_name attached to the object specified by the
* identifier \p loc_id.
*
* \p type_size can be obtained with \c sizeof(), if the data is
* stored in a predefined C struct. Otherwise, it can be obtained
* by calling H5TBget_field_info() if not already known.
*
*/
H5HL_DLL herr_t H5TBread_records(hid_t loc_id, const char *dset_name, hsize_t start, hsize_t nrecords,
size_t type_size, const size_t *dst_offset, const size_t *dst_sizes,
@@ -549,6 +578,10 @@ H5HL_DLL herr_t H5TBdelete_record(hid_t loc_id, const char *dset_name, hsize_t s
* \details H5TBinsert_record() inserts records into the middle of the table
* ("pushing down" all the records after it)
*
* \p dst_size can be obtained with \c sizeof() if the predefined C
* structure is available, otherwise, use H5Tget_size() on the
* compound datatype.
*
*/
H5HL_DLL herr_t H5TBinsert_record(hid_t loc_id, const char *dset_name, hsize_t start, hsize_t nrecords,
size_t dst_size, const size_t *dst_offset, const size_t *dst_sizes,
src/H5FDonion.c
+1 -1
View File
@@ -1154,7 +1154,7 @@ H5FD__onion_open(const char *filename, unsigned flags, hid_t fapl_id, haddr_t ma
* We're getting this buffer from a fixed-size array in a struct, which
* will be garbage and not null-terminated if the user isn't careful.
* Be careful of this and do strndup first to ensure strdup gets a
* null-termianted string (HDF5 doesn't provide a strnlen call if you
* null-terminated string (HDF5 doesn't provide a strnlen call if you
* don't have one).
*/
if (NULL ==
src/H5Fsuper_cache.c
+54
View File
@@ -521,12 +521,36 @@ H5F__cache_superblock_deserialize(const void *_image, size_t len, void *_udata,
udata->btree_k[H5B_CHUNK_ID] = chunk_btree_k;
/* Remainder of "variable-sized" portion of superblock */
/* Check whether the image pointer will be out of bounds */
if (H5_IS_BUFFER_OVERFLOW(image, H5F_sizeof_addr(udata->f) * 4, end))
HGOTO_ERROR(H5E_FILE, H5E_OVERFLOW, NULL, "image pointer is out of bounds");
/* Get and verify base address, delay additional verification */
H5F_addr_decode(udata->f, (const uint8_t **)&image, &sblock->base_addr /*out*/);
if (!H5_addr_defined(sblock->base_addr))
HGOTO_ERROR(H5E_FILE, H5E_BADVALUE, NULL, "base address is undefined");
/* Get extension address, delay verification until stored eof is avail */
H5F_addr_decode(udata->f, (const uint8_t **)&image, &sblock->ext_addr /*out*/);
/* Get and verify stored eof */
H5F_addr_decode(udata->f, (const uint8_t **)&image, &udata->stored_eof /*out*/);
if (!H5_addr_defined(udata->stored_eof))
HGOTO_ERROR(H5E_FILE, H5E_BADVALUE, NULL, "stored EOF address is undefined");
if (udata->stored_eof == 0)
HGOTO_ERROR(H5E_FILE, H5E_BADVALUE, NULL, "stored EOF address cannot be 0");
/* Get driver address */
H5F_addr_decode(udata->f, (const uint8_t **)&image, &sblock->driver_addr /*out*/);
if (H5_addr_defined(sblock->driver_addr) && sblock->driver_addr >= udata->stored_eof)
HGOTO_ERROR(H5E_FILE, H5E_BADVALUE, NULL, "driver info block address exceeds end of file");
/* Validate base and extension addresses against stored_eof */
if (sblock->base_addr >= udata->stored_eof)
HGOTO_ERROR(H5E_FILE, H5E_BADVALUE, NULL, "base address exceeds stored EOF");
if (H5_addr_defined(sblock->ext_addr) && sblock->ext_addr >= udata->stored_eof)
HGOTO_ERROR(H5E_FILE, H5E_BADVALUE, NULL, "superblock extension address exceeds stored EOF");
/* Allocate space for the root group symbol table entry */
if (sblock->root_ent)
@@ -579,10 +603,40 @@ H5F__cache_superblock_deserialize(const void *_image, size_t len, void *_udata,
HGOTO_ERROR(H5E_FILE, H5E_OVERFLOW, NULL, "image pointer is out of bounds");
/* Base, superblock extension, end of file & root group object header addresses */
/* Get and verify base address, delay additional verification */
H5F_addr_decode(udata->f, (const uint8_t **)&image, &sblock->base_addr /*out*/);
if (!H5_addr_defined(sblock->base_addr))
HGOTO_ERROR(H5E_FILE, H5E_BADVALUE, NULL, "base address is undefined");
/* Get extension address, delay verification until stored eof is avail */
H5F_addr_decode(udata->f, (const uint8_t **)&image, &sblock->ext_addr /*out*/);
/* Get and verify stored eof */
H5F_addr_decode(udata->f, (const uint8_t **)&image, &udata->stored_eof /*out*/);
if (!H5_addr_defined(udata->stored_eof))
HGOTO_ERROR(H5E_FILE, H5E_BADVALUE, NULL, "stored EOF address is undefined");
if (udata->stored_eof == 0)
HGOTO_ERROR(H5E_FILE, H5E_BADVALUE, NULL, "stored EOF address cannot be 0");
/* Get and verify root address */
H5F_addr_decode(udata->f, (const uint8_t **)&image, &sblock->root_addr /*out*/);
if (!H5_addr_defined(sblock->root_addr))
HGOTO_ERROR(H5E_FILE, H5E_BADVALUE, NULL, "root address is undefined");
if (sblock->root_addr == 0)
HGOTO_ERROR(H5E_FILE, H5E_BADVALUE, NULL, "root address cannot be 0");
/* Validate addresses against stored_eof.
Skip for VFDs that don't use absolute file offsets */
if (H5F_HAS_FEATURE(udata->f, H5FD_FEAT_DEFAULT_VFD_COMPATIBLE)) {
if (sblock->base_addr >= udata->stored_eof)
HGOTO_ERROR(H5E_FILE, H5E_BADVALUE, NULL, "base address exceeds stored EOF");
if (sblock->root_addr >= (udata->stored_eof - sblock->base_addr))
HGOTO_ERROR(H5E_FILE, H5E_BADVALUE, NULL, "root group address beyond stored EOF");
if (H5_addr_defined(sblock->ext_addr) &&
sblock->ext_addr >= (udata->stored_eof - sblock->base_addr))
HGOTO_ERROR(H5E_FILE, H5E_BADVALUE, NULL, "superblock extension address exceeds stored EOF");
}
/* checksum verification already done in verify_chksum cb */
src/H5Ppublic.h
+11
View File
@@ -5763,6 +5763,17 @@ H5_DLL herr_t H5Pset_mdc_image_config(hid_t plist_id, H5AC_cache_image_config_t
* larger than the page buffer size, the subsequent call to H5Fcreate()
* using the \p plist_id will fail.
*
* The arguments min_meta_perc and min_raw_perc are to prevent one type
* of data from evicting hot pages of the other type, that is, pushing
* them out of the buffer. Setting a minimum percentage for each type
* reserves a portion of the page buffer for that type, ensuring both
* metadata and raw data can maintain a presence in the buffer.
*
* The following constraints apply to min_meta_perc and min_raw_perc:
* - Each must be between 0 and 100 inclusive
* - Their sum must not exceed 100, that is, together they can't reserve
* more than the entire page buffer.
*
* \note As of HDF5 1.14.4, this property will be ignored when an existing
* file is being opened and the file space strategy stored in the
* file isn't paged. This was previously a failure.
src/H5VM.c
+1 -1
View File
@@ -1308,7 +1308,7 @@ done:
* Function: H5VM_memcpyvv
*
* Purpose: Given source and destination buffers in memory (SRC & DST)
* copy sequences of from the source buffer into the destination
* copy sequences from the source buffer into the destination
* buffer. Each set of sequences has an array of lengths, an
* array of offsets, the maximum number of sequences and the
* current sequence to start at in the sequence.